Learning Lineage-guided Geodesics with Finsler Geometry

Single-cell snapshot data can resolve a continuum of cellular states but do not uniquely determine the dynamics governing transitions between them. However, additional dynamical information can often be encoded in a cell-cell Markov transition kernel. Existing generative approaches for single cell trajectory inference either infer transport only from population marginals, impose a symmetric geometry on the state space, or incorporate directionality through a single velocity vector at each observed state. We introduce Finsler Flow Matching (FFM), a framework for learning continuous stochastic dynamics from discrete Markov transition graphs. We use the first and second local moments to construct a Finsler structure motivated by the Freidlin--Wentzell action, where the second moment determines anisotropic accessibility and the first moment introduces a preferred direction of motion. We learn neural approximations of the resulting directed geodesics, use their Finsler cost to construct source-target couplings, and define geometry-aware stochastic conditional paths that can be distilled into a continuous generative process through simulation-free score and flow matching. Across synthetic and single-cell trajectory inference benchmarks, FFM improves recovery of withheld intermediate populations, particularly when the transition dynamics are strongly directional or anisotropic. Our results provide a principled route from discrete transition probabilities to continuous generative dynamics while retaining both directional and diffusive structure.

Trajectory inference is a fundamental problem in many scientific domains: given a collection of unpaired snapshots of observations at discrete time points, the goal is to generate smooth trajectories that best resemble and interpolate the data. Existing algorithms exhibit computational challenges: they either rely on preprocessing subroutines to enforce smoothness or on simulation-based training objectives, both of which can be expensive. In order to overcome these limitations, we propose a new algorithm called Acceleration Matching (AM). Our approach consists of lifting the original interpolation problem to phase space and then regressing onto an explicit conditional acceleration field that induces random, smooth trajectories that agree with the prescribed marginals. Importantly, our resulting training algorithm only requires positional data, avoids trajectory simulation during training, and is devoid of expensive preprocessing. We provide ample numerical evidence suggesting that AM is competitive with or superior to existing algorithms on several benchmark problems from the existing literature.

The geometry of generative models serves as the basis for interpolation, model inspection, and more. Unfortunately, most generative models lack a principal notion of geometry without restrictive assumptions on either the model or the data dimension. In this paper, we construct a general geometry compatible with different metrics and probability distributions to analyze generative models that do not require additional training. We consider curves analogous to geodesics constrained to a suitable data distribution aimed at targeting high-density regions learned by generative models. We formulate this as a (pseudo)-metric and prove that this corresponds to a Newtonian system on a Riemannian manifold. We show that shortest paths in our framework can be characterized by a system of ordinary differential equations, which locally corresponds to geodesics under a suitable Riemannian metric. Numerically, we derive a novel algorithm to efficiently compute shortest paths and generalized Fréchet means. Quantitatively, we show that curves using our metric traverse regions of higher density than baselines across a range of models and datasets.